Analysis of gene expression and gene set data http://webtools.systemsmedicine.jp/exatlas/
Developed at the National Institute on Aging, NIA/NIH, Baltimore USA. Programmer Alexei Sharov sharov@comcast.net
ExAtlas is a tool for meta-analysis of gene expression data. In contrast to other software, it compares multi-component data sets and generates results for all combinations (e.g., all gene expression profiles vs. all GO annotations). Main functions are: (1) standard meta-analysis (fixed and random effects, z-score, Fisher's method; analysis of (2) global correlations between gene expression data sets; (3) gene set enrichment; (4) gene set overlap; (5) gene association (Expected Proportion of False Positives, EPFP); (6) statistical analysis of gene expression (ANOVA, PCA, FDR). Results are presented graphically as heatmaps, bar-charts, or 3-D images (PCA). Gene expression data is extracted automatically from GEO/NCBI database. Several most popular public data sets (e.g., GNF, Gene Ontology, KEGG, GAD phenotypes) are pre-loaded and can be used for functional annotations.
This software is provided "AS IS". Programmer makes no warranties, express or implied, including no representation or warranty with respect to the performance of the software and derivatives or their safety, effectiveness, or commercial viability. Programmer does not warrant the merchantability or fitness of the software and derivatives for any particular purpose, or that they may be exploited without infringing the copyrights, patent rights or property rights of others. Programmer shall not be liable for any claim, demand or action for any loss, harm, illness or other damage or injury arising from access to or use of the software or associated information, including without limitation any direct, indirect, incidental, exemplary, special or consequential damages. This software program may not be sold, leased, transferred, exported or otherwise disclaimed to anyone, in whole or in part, without the prior written consent of programmer.
DIRECTORY STRUSTURE
ExAtlas = exatlas.ini file
ExAtlas/exatlas = html files
ExAtlas/exatlas/bin = exatlas.cgi (CGI program)
ExAtlas/exatlas/images = images
ExAtlas/exatlas/output = writable directory for output files
ExAtlas/exatlas/download
ExAtlas/exatlasInfo/bin = other programs (C, perl), C-programs should be compiled here
ExAtlas/exatlas/info = writable directory for personal config files, login.txt
ExAtlas/exatlas/data = writable directory for data files
Compile C-programs in ExAtlas/exatlasInfo/bin:
gcc anova_oneway.c -lm -o anova_oneway
gcc togif.c -lm -o togif
gcc correlation_exatlas.c -lm -o correlation_exatlas
gcc norm_new.c -lm -o norm_new
gcc page_exatlas.c -lm -o page_exatlas
gcc pairwise.c -lm -o pairwise
gcc pca.c -lm -o pca
Configure two accounts to your name: administrator, public. Edit file login.txt and put your name and email address Log into ExAtlas and change your passwords for both account. Create your own working account in ExAtlas